Population Genomics Refines Population Structure and Individual Stock Assignment in Atlantic and Mediterranean Swordfish (Xiphias gladius).
21 affiliations
- 1Dipartimento di Scienze della Vita e dell'Ambiente, Universita' Politecnica delle Marche, 60131 Ancona, Italy.
- 2Fisheries and Oceans Canada, St. Andrews Biological Station, 125 Marine Science Drive, St. Andrews, NB E5B 0E4, Canada.
- 3Instituto Português do Mar e da Atmosfera (IPMA), Av. 5 de Outubro s/n, 8700-305 Olhão, Portugal.
- 4Centro de Ciências do Mar da Universidade do Algarve (CCMar), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
- 5Instituto de Oceanografia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n Dois Irmãos, 52171-900 Recife, PE, Brazil.
- 6Centro Oceanográfico de Málaga, Instituto Español de Oceanografía (IEO-CSIC), Puerto Pesquero s/n, 29640 Fuengirola, Spain.
- 7AquaBioTech Group, Central Complex, Naggar Street, Targa Gap, MST 1761 Mosta, Malta.
- 8MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34203 Sète, France.
- 9Department of Earth, Environment and Life Sciences, University of Genoa, Corso Europa, 26, 16132 Genova, Italy.
- 10Laboratório de Recursos Pesqueiros Demersais e Cefalópodes, Instituto de Oceanografia, Universidade Federal do Rio Grande, Av. Itália, sn, Campus Carreiros, 96203-900 Rio Grande, RS, Brazil.
- 11OCEANIS SRL, 80056 Ercolano, Italy.
- 12Sequentia Biotech SL, 08005 Barcellona, Spain.
- 13Department of Environmental Biology and Fishery Science, National Taiwan Ocean University, Keelung 20224, Taiwan.
- 14Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa.
- 15Hellenic Centre for Marine Research, Athens Sounio Ave., P.O. Box 712, Anavyssos, 19013 Attiki, Greece.
- 16Instituto Oceanográfico de Venezuela, Universidad de Oriente, A.P. 204, 6101 Cumana, Venezuela.
- 17Ministry of Fisheries and Marine Resources, National Marine Information and Research Centre, Swakopmund P.O. Box 912, Namibia.
- 18Aquastudio Research Institute, Via Trapani, 6, 98121 Messina, Italy.
- 19Department of Life Science and Environment, University of Cagliari, Via Fiorelli 1, 09126 Cagliari, Italy.
- 20UNIMAR Società Cooperative, Via Nazionale, 243, 00184 Roma, Italy.
- 21ICCAT Secretariat, Calle Corazón de Maria 8, Planta 6, 28002 Madrid, Spain.
Abstract
Swordfish (Xiphias gladius) is managed in the Atlantic Ocean and Mediterranean Sea as three major stocks, although their correspondence with underlying genomic population structure remains uncertain. Here, we combined a newly assembled reference genome with ddRAD sequencing of 575 swordfish from 14 Atlantic and Mediterranean areas to characterize genomic population structure and genetic differentiation relative to the current ICCAT management framework, evaluate individual stock assignment and ancestry across management boundaries, and compare genetic-diversity patterns among stocks and sampling areas. After quality control, 504 individuals were retained, with 26,324 SNPs used for diversity analyses and 15,049 LD-pruned SNPs for population-structure and assignment analyses. Multivariate analyses, pairwise differentiation, AMOVA, and ADMIXTURE consistently identified strong Mediterranean-Atlantic differentiation, whereas North and South Atlantic swordfish showed much weaker and partly continuous genomic structure. Formal stock identification, DAPC, and ADMIXTURE consistently assigned 11 individuals from Portugal and the Canary Islands to the Mediterranean stock. Within the Atlantic, ancestry patterns were more diffuse and included individuals with assignments discordant with their a priori management stock. Heterozygosity was broadly similar among stocks, whereas rarefied allelic richness was lower in the Mediterranean than in either Atlantic stock. Overall, the current management framework captures the major Mediterranean-Atlantic differentiation but only partially reflects the weaker genomic structure within the Atlantic. These findings show that population-genomic analyses can refine stock-structure inference and individual assignment while providing complementary information for swordfish assessment and monitoring.
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BibTeX
@article{gioacchini2026population,
title = {{Population Genomics Refines Population Structure and Individual Stock Assignment in Atlantic and Mediterranean Swordfish (Xiphias gladius).}},
author = {Giorgia Gioacchini and Kyle Gillespie and Daniela Rosa and Sara Filippi and Luca Marisaldi and Dheeraj Busawon and Natalia Bezerra and Paulo Travassos and Hilário Tiago Campello and Fábio Hissa Vieira Hazin and David Macías and Alexia Gallucci and Francois Poisson and Fulvio Garibaldi and Luis Gustavo Cardoso and Luigi Pappalardo and Paolo Pignalosa and Riccardo Aiese Cigliano and Su Nan-Jay and Dan Parker and George Tserpes and Freddy Arocha and Taimi Shikongo and Tommaso Righi and Andrea Splendiani and Antonio Di Natale and Piero Addis and Adriano Mariani and Miguel Neves Dos Santos and Rui Coelho and Alex Hanke and Oliana Carnevali},
journal = {International journal of molecular sciences},
year = {2026},
month = sep,
doi = {10.3390/ijms27198612},
url = {https://europepmc.org/article/MED/42883862},
note = {CC BY},
}
RIS
TY - JOUR
TI - Population Genomics Refines Population Structure and Individual Stock Assignment in Atlantic and Mediterranean Swordfish (Xiphias gladius).
AU - Giorgia Gioacchini
AU - Kyle Gillespie
AU - Daniela Rosa
AU - Sara Filippi
AU - Luca Marisaldi
AU - Dheeraj Busawon
AU - Natalia Bezerra
AU - Paulo Travassos
AU - Hilário Tiago Campello
AU - Fábio Hissa Vieira Hazin
AU - David Macías
AU - Alexia Gallucci
AU - Francois Poisson
AU - Fulvio Garibaldi
AU - Luis Gustavo Cardoso
AU - Luigi Pappalardo
AU - Paolo Pignalosa
AU - Riccardo Aiese Cigliano
AU - Su Nan-Jay
AU - Dan Parker
AU - George Tserpes
AU - Freddy Arocha
AU - Taimi Shikongo
AU - Tommaso Righi
AU - Andrea Splendiani
AU - Antonio Di Natale
AU - Piero Addis
AU - Adriano Mariani
AU - Miguel Neves Dos Santos
AU - Rui Coelho
AU - Alex Hanke
AU - Oliana Carnevali
PY - 2026
DA - 2026/09/26
JO - International journal of molecular sciences
DO - 10.3390/ijms27198612
UR - https://europepmc.org/article/MED/42883862
AB - Swordfish (Xiphias gladius) is managed in the Atlantic Ocean and Mediterranean Sea as three major stocks, although their correspondence with underlying genomic population structure remains uncertain. Here, we combined a newly assembled reference genome with ddRAD sequencing of 575 swordfish from 14 Atlantic and Mediterranean areas to characterize genomic population structure and genetic differentiation relative to the current ICCAT management framework, evaluate individual stock assignment and ancestry across management boundaries, and compare genetic-diversity patterns among stocks and sampling areas. After quality control, 504 individuals were retained, with 26,324 SNPs used for diversity analyses and 15,049 LD-pruned SNPs for population-structure and assignment analyses. Multivariate analyses, pairwise differentiation, AMOVA, and ADMIXTURE consistently identified strong Mediterranean-Atlantic differentiation, whereas North and South Atlantic swordfish showed much weaker and partly continuous genomic structure. Formal stock identification, DAPC, and ADMIXTURE consistently assigned 11 individuals from Portugal and the Canary Islands to the Mediterranean stock. Within the Atlantic, ancestry patterns were more diffuse and included individuals with assignments discordant with their a priori management stock. Heterozygosity was broadly similar among stocks, whereas rarefied allelic richness was lower in the Mediterranean than in either Atlantic stock. Overall, the current management framework captures the major Mediterranean-Atlantic differentiation but only partially reflects the weaker genomic structure within the Atlantic. These findings show that population-genomic analyses can refine stock-structure inference and individual assignment while providing complementary information for swordfish assessment and monitoring.
SN - 1422-0067
SN - 1661-6596
ER -